doc: Improve Info categories.

* doc/guix.texi: Change main category to "System administration".  Fix
syntax of subnodes.  Add entries for 'guix pull' and 'guix gc'.  Add
"Emacs" category.

build: Use (guix grafts) as needed.

This is a followup to 7adf9b8.

* build-aux/check-final-inputs-self-contained.scm: Use (guix grafts).
* build-aux/check-available-binaries.scm: Likewise.

gnu: youtube-dl: Update to 2016.03.01.

* gnu/packages/video.scm (youtube-dl): Update to 2016.03.01.

gnu: mpv: Update to 0.16.0.

* gnu/packages/video.scm (mpv): Update to 0.16.0.

gnu: perl: Replace with patched version [fixes CVE-2016-2381].

* gnu/packages/patches/perl-CVE-2016-2381.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/perl.scm (perl)[replacement]: New field.
(perl-fixed): New variable.
* gnu/packages/commencement.scm (perl-boot0)[replacement]: New field.

gnu: irssi: Support proxy, socks, bot.

* gnu/packages/irc.scm (irssi)[arguments]: Add configure flags to
support proxy, socks and bot.

gnu: irssi: Update to 0.8.18.

* gnu/packages/irc.scm (irssi): Update to 0.8.18.
[source]: Update uri.

build: Build (guix import github) only when Guile-JSON is available.

Reported by Justus Winter <justus@gnupg.org>.

* Makefile.am (MODULES): Add guix/import/github.scm only when
HAVE_GUILE_JSON.

po: Drop removed file 'weechat.scm'.

Fixes <http://bugs.gnu.org/22888>.
weechat has been merged into 'irc.scm' in e288f007.

* po/packages/POTFILES.in: Drop removed file 'weechat.scm'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

system: GRUB menu entry says "beta" instead of "alpha"

* gnu/system.scm (kernel->grub-label): Change "alpha" to "beta'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

system: Add rfkill to '%base-packages'.

* gnu/system.scm (%base-packages): Add RFKILL.

gnu: python-pysam: Move cython and setuptools to native inputs.

* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.

gnu: deeptools: Update to 2.1.1.

* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".

gnu: deeptools: Change "propagated-inputs" to "inputs".

* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.

gnu: Add python-pybigwig.

* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
  New variables.

gnu: python-pysam: Update to 0.8.4.

* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.

gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.

* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
  ...here.

lint: derivation: Disable grafts, but check replacements.

* guix/scripts/lint.scm (check-derivation): Pass #:graft? #f.  When
'package-replacement' exists, compute its derivation.

gnu: Add procmail.

 * gnu/packages/patches/procmail-ambiguous-getline-debian.patch: New file.
 * gnu-system.am (dist_patch_DATA): Add it.
 * gnu/packages/mail.scm (procmail): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>

guix build: -S returns the replacement's source.

Reported by Mark H Weaver.

* guix/scripts/build.scm (options->derivations): When SRC and GRAFT? are
true, use the source of P's replacement.
* tests/guix-build.sh: Add test.